The nucleotide sequences of cDNA and genomic DNA clones for NK-1, NK-2, NK- 3 and NK-4 homeobox genes from Drosophila melanogaster were determined. NK-1 is expressed in small subsets of neurons and striated muscle cells in each thoracic and abdominal segment and in cells in the head. Genomic DNA was cloned from monkey and rat that corresponds to the Drosophila NK-1 homeobox DNA. Nucleotide sequence analysis showed that the amino acid sequences of the homeobox domains of monkey and rat are identical to that of the Drosophila NK-1 homeobox. NK-2 mRNA expression begins at the cellular blastoderm stage in the ventrolateral portion of the embryo as these cells become committed to the neuroectodermal pathway of development, which is the first step in the developmental program that leads to the formation of the nervous system. In 12 hr and older embryos NK-2 gene expression also was found in cells associated with the midgut. NK-3 and NK-4 are neighboring homeobox genes. NK-3 is expressed transiently in visceral mesoderm in 6-12 hr embryos in a segmentally repeated pattern. NK-4 mRNA also is expressed transiently starting as mesodermal cells appear during gastrulation (3 hr) and disappearing after 7.5 hr. Genomic DNA clones corresponding to 7 novel mouse homeobox genes were obtained and the nucleotide sequences of the homeobox regions were determined. Additional nucleotide sequence information was obtained for 2 of the 7 clones. Two novel species of Pou box-homeobox cDNA were cloned and the Pou box-homeobox regions were sequenced. Clones of mouse genomic DNA fragments with enhancer activity in N18TG2 mouse neuroblastoma cells were obtained by a selection method. CTF/NF-1 and LVc proteins extracted from N18TG2 nuclei bind to sites in cloned N1 DNA and function as enhancers. cDNA clones were obtained that correspond to species of NG108-15 poly A + RNA that increase in abundance when cells are treated with compounds that elevate cells cAMP. Four of the clones correspond to different regions of mitochondrial DNA, one clone corresponds to secretogranin I, and one corresponds to ribosomal protein S-10 mRNA.